I don't think there are any hard and fast rules, coffee has antioxidants and does help with mood. If it is not causing problems then I would not be worried about it.
Leaky gut is always a problem if you have it. It is caused by pathogens in the gut. The immune system is working to get rid of the infection and as a result puts out chemicals that damage the lining. If the lining is damaged then you get more inflammatory conditions.
The best thing for leaky gut is organic gelatin which has the amino acids that help rebuild the gut lining. Red tea (roobios) and peppermint tea are the best in my opinion.